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fix(snakemake): update to v7.32.4 to make Python 3.11 clients compatible #435

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Feb 1, 2024
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fix(snakemake): update to v7.32.4 to make Python 3.11 clients compatible #435

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2 changes: 1 addition & 1 deletion reana_commons/config.py
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Original file line number Diff line number Diff line change
Expand Up @@ -440,7 +440,7 @@ def default_workspace():
REANA_WORKFLOW_ENGINES = ["yadage", "cwl", "serial", "snakemake"]
"""Available workflow engines."""

REANA_DEFAULT_SNAKEMAKE_ENV_IMAGE = "docker.io/snakemake/snakemake:v6.8.0"
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This change should rather be a feature, not a fix. While it's technically true that we are fixing things for py311 clients, we are also upgrading Snakemake to a new major version, which might affect all clients for all other Python versions. So we should rather bring attention to that. I would suggest putting something like feat(snakemake): upgrade to Snakemake 7.32.4 for the release announcement headline.

REANA_DEFAULT_SNAKEMAKE_ENV_IMAGE = "docker.io/snakemake/snakemake:v7.32.4"
"""Snakemake default job environment image."""

REANA_JOB_CONTROLLER_CONNECTION_CHECK_SLEEP = float(
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24 changes: 16 additions & 8 deletions reana_commons/snakemake.py
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Expand Up @@ -93,7 +93,7 @@ def _create_snakemake_dag(
if workdir:
workflow.workdir(workdir)

workflow.include(snakefile=snakefile, overwrite_first_rule=True)
workflow.include(snakefile=snakefile, overwrite_default_target=True)
workflow.check()

# code copied and adapted from `snakemake.workflow.Workflow.execute()`
Expand All @@ -113,16 +113,20 @@ def files(items):
else:

def files(items):
relpath = (
lambda f: f
if os.path.isabs(f) or f.startswith("root://")
else os.path.relpath(f)
)
def relpath(f):
return (
f
if os.path.isabs(f) or f.startswith("root://")
else os.path.relpath(f)
)

return map(relpath, filterfalse(workflow.is_rule, items))

if not kwargs.get("targets"):
targets = (
[workflow.first_rule] if workflow.first_rule is not None else list()
[workflow.default_target]
if workflow.default_target is not None
else list()
)

prioritytargets = kwargs.get("prioritytargets", [])
Expand Down Expand Up @@ -157,7 +161,11 @@ def files(items):
omitrules=omitrules,
)

workflow.persistence = Persistence(dag=dag)
if hasattr(workflow, "_persistence"):
workflow._persistence = Persistence(dag=dag)
else:
# for backwards compatibility (Snakemake < 7 for Python 3.6)
workflow.persistence = Persistence(dag=dag)
Comment on lines +164 to +168
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This is needed to also support Python 3.6, that uses a Snakemake version (6.15) in which the new default_target directive is present, but internally persistence had not been replaced by _persistence yet in the snakemake.Workflow class. I think this approach of directly checking the attribute (rather than checking, say, the Python version) is correct, but I'm more than happy to get advice on how to do this better, if you think there's a more appropriate way!

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I think this is good and I prefer it over checking Snakemake/Python version

dag.init()
dag.update_checkpoint_dependencies()
dag.check_dynamic()
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8 changes: 4 additions & 4 deletions setup.py
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Expand Up @@ -35,13 +35,13 @@
"yadage": ["adage~=0.10.1", "yadage~=0.20.1", "yadage-schemas~=0.10.6"],
"cwl": ["cwltool==3.1.20210628163208"],
"snakemake": [
"snakemake==6.8.0 ; python_version<'3.12'",
"snakemake==7.9.0 ; python_version>='3.12'",
"snakemake==6.15.5 ; python_version<'3.7'", # Snakemake v7 requires Python 3.7+
"snakemake==7.32.4 ; python_version>='3.7'",
"tabulate<0.9",
],
"snakemake_reports": [
"snakemake[reports]==6.8.0 ; python_version<'3.12'",
"snakemake[reports]==7.9.0 ; python_version>='3.12'",
"snakemake==6.15.5 ; python_version<'3.7'",
"snakemake==7.32.4 ; python_version>='3.7'",
"pygraphviz<1.8",
"tabulate<0.9", # tabulate 0.9 crashes snakemake, more info: https://github.com/snakemake/snakemake/issues/1899
],
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1 change: 1 addition & 0 deletions tests/conftest.py
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Expand Up @@ -20,6 +20,7 @@ def dummy_snakefile():
"results/foo.txt",
"results/bar.txt",
"results/baz.txt"
default_target: True

rule foo:
input:
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4 changes: 0 additions & 4 deletions tests/test_snakemake.py
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Expand Up @@ -17,10 +17,6 @@

def test_snakemake_load(tmpdir, dummy_snakefile):
"""Test that Snakemake metadata is loaded properly."""
if sys.version_info.major == 3 and sys.version_info.minor in (11, 12):
pytest.xfail(
"Snakemake features of reana-client are not supported on Python 3.11"
)
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This should also be removed from tests in reana-client

workdir = tmpdir.mkdir("sub")
# write Snakefile
p = workdir.join("Snakefile")
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